Feature Articles

Structural Biology Underpins R&D Efforts

Information Generated from Struture-Based Programs Finds Niche in Product Development

High-Throughput Screening

Rajarshi Guha, Ph.D., research informatics scientist at NIH Chemical Genomics Center (NCGC), was scheduled to speak at the meeting about his research. NCGC is a high-throughput screening center with expertise in HTS assay development and assay optimization.

Upon receipt of an assay and subsequent optimization, the center screens the Molecular Libraries Small Molecule Repository (MLSMR) of about 400,000 molecules, along with other libraries. “From the primary screening, we get our set of hits and, in some projects, have access to structural information for follow-up structure-activity relationship (SAR) studies,” he explained.

“Our use of structural biology at that point is to identify useful molecular series for secondary screening, and, in some cases, it’s also used to directly elucidate more specific SARs in the lead-optimization process.”

Dr. Guha has focused on linking small molecule ligand SARs with RNAi screening assays to probe novel drug targets. His group is also trying to develop a systems-based approach in which results from RNAi screens are integrated with results from small molecule screens using MLSMR. “We are trying to get more high-resolution information and, for that reason, we are moving to high-content screening on both small molecules and RNAi.”

There is a major challenge in performing such phenotypic matching, though—the mechanism for small molecule hits and RNAi molecule hits differ substantially from one other. “So when a molecule and an siRNA are both identified as active in their respective assays, that doesn’t mean that the small molecule is hitting the same target as that of the RNAi knockdown,” said Dr. Guha.

As a result, Dr. Guha and his team are spending a lot of time performing pilot testing and tweaking their methods of phenotypic matching. “I think there’s a wide scope in this approach, in that, even though high-content imaging screens are time-consuming, the end result is a rich set of data that allows us to go toward a holistic picture of what’s going on at the small molecule level.”

Structure for Stronger Bonding

Avila Therapeutics uses a structure-based platform to discover and then develop covalent inhibitors, a class of drugs that it says has not been well explored by the pharmaceutical industry. Avila’s platform creates molecules that are designed to bind specifically and tightly to their cognate targets and then form a bond with those targets.

A lot of companies create reversible inhibitors that come on and off the target, but Avila’s covalently bonded drugs are different from the pack. “We believe there is a pharmacological advantage in having drugs that actually form a bond and remain on the target—they can achieve better selectivity, they can achieve a longer duration of action, and can lead to fewer side effects,” said Juswinder Singh, Ph.D., co-founder and CSO.

Although covalent inhibitors are not well explored by the pharmaceutical industry, in general, there are a lot of highly successful covalent inhibitors, such as Plavix. “There is a disconnect between the prevalence of covalent drugs and the lack of attention and focus on that area,” says Dr. Singh, who added that there are a few reasons for this lack of attention: prejudice against the actual approach itself, concern about more side effects, and a lack of valid methods to enable discovery of these types of drugs.

According to Dr. Singh, Plavix “was not designed, it was discovered through serendipity. And that is why structural biology becomes an important component because we believe that we can use design algorithms to discover drugs against targets that form specific bonds with them.” Avila discovers these drugs by examining the drug binding sites for residues that are unique to that target, then creating chemistry that will form a bond to that drug target.

At the meeting, Dr. Singh described Avila’s efforts to use its platform to discover hepatitis C virus (HCV) protease inhibitors. Current HCV drugs are susceptible to resistance. “We believe that covalent inhibitors as a mechanism of action can be more active against drug-resistant mutants than reversible inhibitors because, if the covalent inhibitor is on the target long enough to form a bond, that target is inactivated until a new protein is re-synthesized,” he explained.

“We discovered that there was a residue in the HCV protease that did not appear in host proteases that can be acted upon by covalent inhibitors.” This inhibitor is currently in preclinical development.

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Secure Science

Should bans on science education, of the sort imposed on Iranians hoping to study physics and engineering in the United States, encompass other nationals and other fields of study, including biotechnology?

No. Such bans could easily get out of control, preventing the sharing and growth of knowledge.

Yes. The potential, for example, for the development of bioweapons if biotech information gets into the wrong hands must be minimized.

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57.3%

Yes. The potential, for example, for the development of bioweapons if biotech information gets into the wrong hands must be minimized.

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